It generally accepted that cancer results from the accumulation of sequential mutations in a cell that confer a selective growth advantage to the cell. The tumor is a clonal expansion of the cell containing the mutations, and cells within the tumor likely accumulate further mutations during proliferation. This accumulation of mutations results in genetic instability that leads to uncontrolled growth due to hyper-proliferation or insufficient apoptosis. The loss of genomic stability occurs early in the process of carcinogenesis and represents a key molecular step in the development of cancer by providing a permissive environment in which further mutations can accumulate.
Mutations that result in a gain of function (e.g., activation of Ras by mutation at amino acid 12) can result in the development of cancer alone. However, mutations that result in genomic instability are often loss-of-function mutations in genes responsible for DNA repair, cell division cycle checkpoints, cell motility, transcriptional regulation, and apoptosis. These genes are often called tumor-suppressor genes. A large number of genes identified in screens to be involved in cancer have undefined or incompletely defined relationships uniting their structure with their biological function (e.g., BRCA2), making it difficult, if not impossible, to determine which mutations, if any, are deleterious to gene function. Loss of a first allele does not lead directly to cancer, but makes the cell susceptible to increasingly severe consequences upon acquisition of further mutations. For example, loss of a second allele on the same gene, or mutation of another gene in a pathway in which the first mutation occurred can lead to loss of cell cycle control.
Although some cancers have a strong hereditary component, the large majority of cancers are not associated with a specific genetic predisposition. Moreover, a large number of familial cancers associated with loss-of-function of genes (e.g., BRCA1, BRCA2, MLH1, MSH2) may not manifest overt disease until after the individual has produced children. Similarly a number of other later onset diseases that may have a genetic component (e.g., alpha- or beta-synuclein mutations or APO-E variants in Alzheimer's disease, HTT mutations in Huntington disease, and late-onset forms of diseases more commonly known as affecting the young, such as Tay Sachs or cystic fibrosis, that do not manifest overt disease until the individual has produced children.
Large scale analyses have been performed on tumor samples to identify mutations associated with cancer (e.g., Dutt et al., Curr. Opin. Oncol. 2007. 19:43-49; Greenman et al., Nature 2007. 446:153-158; Ottini et al., Ann. Oncol. 2006. 17:vii97-vii102; Sjöblom et al., Science, 2006. 314:268-314; Lea et al., Carcinogenesis 2007. 28:1851-1858, each incorporated herein by reference). However, such analyses were performed on tumor samples or cancer cell lines which have accumulated multiple mutations. For example, analysis of 13,023 genes in 11 breast and 11 colorectal cancers by Sjöblom revealed that individual tumors accumulate about 90 mutant genes, but that only a subset of the mutations contribute to the neoplastic process. Mutations that were germline variants (i.e., present in the patients' genomes at birth) but resulting in no changes in the amino acid sequence of the protein encoded, as well as germline variants identified from the published human sequence present in SNP databases or in two control samples, were disregarded as not being related to cancer. Using these stringent criteria, 189 genes were identified that were mutated with a significant frequency, with an average of 11 genes mutated per tumor. However, despite the identification of such genes and mutations, such a screen does not identify which mutations are deleterious, causing a change of function in the gene product, or are benign. The screens are also not useful for determining which of the less common tumor mutations or which of the germline variants result in an alteration of function that results in a greater susceptibility to disease in a subject as compared to the general population.